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ksumngs
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yavsap
Yet Another Viral Subspecies Analysis Pipeline
https://ksumngs.github.io/yavsap
MIT License
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feat: Add python-based envrc
#52
MillironX
closed
4 months ago
1
Add Variant table to MultiQC report
#51
MillironX
closed
1 year ago
1
Add genome annotations
#50
MillironX
closed
1 year ago
2
Add multi-strand support
#49
MillironX
closed
1 year ago
1
Update e-direct containers
#48
MillironX
closed
1 year ago
1
[Feature]: Add workflow for downloading reference genomes
#47
MillironX
opened
2 years ago
0
Update nf-core template to v1.4.0
#46
MillironX
closed
2 years ago
1
Template_merge
#45
MillironX
closed
2 years ago
1
[Feature]: Add ability to use files as a reference genome
#44
MillironX
opened
2 years ago
0
[Feature]: Finish help text for Visualizer sections
#43
MillironX
closed
2 years ago
0
[Feature]: Add genome annotations
#42
MillironX
closed
1 year ago
0
[Bug]: No visualizer output for Nanopore reads
#41
MillironX
closed
2 years ago
1
Switch visualizer to static page
#40
MillironX
closed
2 years ago
1
Bump moment from 2.29.1 to 2.29.2 in /visualizer
#39
dependabot[bot]
closed
2 years ago
4
Hotfix/0.6.5-alpha
#38
MillironX
closed
2 years ago
1
[Hotfix]: Re-add Kraken2 dynamic memory allocation
#37
MillironX
closed
2 years ago
1
Hotfix/0.6.3 alpha
#36
MillironX
closed
2 years ago
4
Feature/nf-core_modules
#35
MillironX
closed
2 years ago
2
Distinguish between 'paired-end' and 'Illumina' reads
#34
MillironX
closed
2 years ago
0
Add NanoStat QC reporting
#33
MillironX
closed
2 years ago
0
Feature/artitrary-genomes
#32
MillironX
closed
2 years ago
0
Add ability to use samplesheets
#31
MillironX
closed
2 years ago
0
Fix random seed in RNG-based processes
#30
MillironX
closed
2 years ago
0
Feature/tree-reroot
#29
MillironX
closed
2 years ago
0
[Feature]: Add a one-click Visualizer setup script
#28
MillironX
closed
2 years ago
3
[Feature]: Disinguish between 'Illumina' and 'Paired-end' reads
#27
MillironX
closed
2 years ago
0
[Feature]: Change the visualizer to use NPM modules in a more "traditional" way
#26
MillironX
closed
2 years ago
0
[Feature]: Make compatible with multi-strand viruses
#25
MillironX
closed
1 year ago
0
[Feature]: Add genome presets for more viruses
#24
MillironX
opened
2 years ago
3
[Feature]: Allow passing arbitrary genome list
#23
MillironX
closed
2 years ago
0
[Feature]: Extract processes used in common with v-met into modules
#22
MillironX
closed
2 years ago
0
[Feature]: Allow using samplesheets
#21
MillironX
closed
2 years ago
0
Add quality cutoff parameters for phylogenetic trees
#20
MillironX
closed
2 years ago
0
Automatically document parameters and functions
#19
MillironX
closed
2 years ago
0
Add VCF output for Illumina samples
#18
MillironX
closed
2 years ago
0
Feature/pbsim
#17
MillironX
closed
2 years ago
0
Feature/haplink0.4
#16
MillironX
closed
2 years ago
0
Feature/ncbi-dl
#15
MillironX
closed
2 years ago
0
[Feature]: Add an indication of which genotype the sample (most likely) belongs to
#14
MillironX
closed
2 years ago
0
[Feature]: Allow for setting of random seed
#13
MillironX
closed
2 years ago
1
[Feature]: Add reroot capability to phylogenetic tree in visualizer
#12
MillironX
closed
2 years ago
0
[Feature]: Add tree quality as iteration metric for RAxML-NG phylogenies
#11
MillironX
closed
2 years ago
1
[Feature]: Add self-documentation to pipeline
#10
MillironX
closed
2 years ago
0
Fix container definition for read realignment
#9
MillironX
closed
2 years ago
0
Move file copying to Nextflow processes
#8
MillironX
closed
2 years ago
0
Hotfix 0.3.1-alpha
#7
MillironX
closed
2 years ago
0
pipeline: Realign reads based on closest reference genome
#6
MillironX
closed
2 years ago
0
parameterization: Allow skipping read trimming and QC
#5
MillironX
closed
2 years ago
0
[Feature]: Conform to style guide
#4
MillironX
closed
2 years ago
0
performance: Use containers for all processes
#3
MillironX
closed
2 years ago
0
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